LAMMPS (18 Feb 2013)
# 2d indenter simulation

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region		box block 0 20 0 10 -0.25 0.25
create_box	2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
  2 by 2 by 1 MPI processor grid
create_atoms	1 box
Created 420 atoms

mass		1 1.0
mass		2 1.0

# LJ potentials

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0 2.5

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
60 atoms in group lower
group		mobile subtract all lower
360 atoms in group mobile
set		group lower type 2
  60 settings made for type

# initial velocities

compute	  	new mobile temp
velocity	mobile create 0.2 482748 temp new
fix		1 all nve
fix		2 lower setforce 0.0 0.0 0.0
fix		3 all temp/rescale 100 0.1 0.1 0.01 1.0

# run with indenter

timestep	0.003
variable	k equal 1000.0/xlat
variable        y equal "13.0*ylat - step*dt*0.02*ylat"

fix		4 all indent $k sphere 10 v_y 0 5.0
fix		4 all indent 882.84928691481343321 sphere 10 v_y 0 5.0
fix		5 all enforce2d

thermo		1000
thermo_modify	temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)

#dump		1 all atom 250 dump.indent

#dump		1 all image 1000 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	1 pad 5

run		30000
Memory usage per processor = 2.06495 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0          0.2   -3.1727576            0   -3.0018052    -1.436185    444.53333 
    1000   0.11573595   -3.0964873            0   -2.9975606  -0.20448672    441.83732 
    2000   0.11519605   -3.0960246            0   -2.9975594  -0.38133491    442.33058 
    3000   0.11367906   -3.0839597            0   -2.9867912  -0.42579765    444.59119 
    4000   0.11618844   -3.0860897            0   -2.9867762 -0.041580916    439.84614 
    5000   0.11327789   -3.0848614            0   -2.9880358  -0.48898867    446.19202 
    6000   0.12058424   -3.0869438            0    -2.983873  0.011477134    440.56887 
    7000   0.11772522   -3.0833477            0   -2.9827207 -0.090378245    442.56787 
    8000   0.12533514   -3.0970033            0   -2.9898715   0.13263189    441.23478 
    9000    0.1198683   -3.0867062            0   -2.9842473   0.34046664     439.4706 
   10000   0.12234014   -3.0835007            0   -2.9789291   0.28399731    441.94307 
   11000   0.11082436   -3.0754796            0   -2.9807511   0.62194284    441.32012 
   12000   0.10842719   -3.0646379            0   -2.9719584   0.65383569    442.64668 
   13000   0.11686417   -3.0600388            0   -2.9601477    1.0041123    438.50135 
   14000   0.12557378   -3.0570017            0    -2.949666   0.85709167    442.10189 
   15000   0.11934084   -3.0498848            0   -2.9478768    1.0392199    451.74396 
   16000   0.12576904   -3.0452178            0   -2.9377152    1.3479499    441.27019 
   17000   0.11546522   -3.0348362            0    -2.936141    1.6318206     439.4846 
   18000   0.12148311   -3.0221147            0   -2.9182755    1.6088802    449.25447 
   19000     0.118843    -3.003677            0   -2.9020946    1.5201603    447.11853 
   20000   0.11165592   -3.0037968            0   -2.9083575    1.4074727    461.75512 
   21000   0.11360385   -2.9898251            0   -2.8927209    1.1326435    473.96384 
   22000   0.12150985   -3.0248097            0   -2.9209477   0.78906514     473.4399 
   23000   0.11900756   -3.0140794            0   -2.9123563    1.2011762    469.94964 
   24000   0.12144629   -3.0209952            0   -2.9171876   0.75868599    473.27056 
   25000   0.12502653   -3.0209271            0   -2.9140592   0.69048742    484.86502 
   26000   0.12040444    -3.021456            0   -2.9185388   0.21874131    486.96835 
   27000   0.11960292   -3.0422633            0   -2.9400313   0.37183014    486.93936 
   28000   0.11652365   -3.0437678            0   -2.9441678   0.65795683     483.2875 
   29000   0.11671309    -3.044343            0   -2.9445811   0.81258278    482.40921 
   30000    0.1220056   -3.0408195            0   -2.9365338    0.8072655    486.26501 
Loop time of 0.963257 on 4 procs for 30000 steps with 420 atoms

Pair  time (%) = 0.449727 (46.6882)
Neigh time (%) = 0.0182621 (1.89587)
Comm  time (%) = 0.241803 (25.1026)
Outpt time (%) = 0.000499487 (0.051854)
Other time (%) = 0.252965 (26.2614)

Nlocal:    105 ave 120 max 89 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost:    91.5 ave 98 max 85 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs:    904 ave 1090 max 721 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 3616
Ave neighs/atom = 8.60952
Neighbor list builds = 615
Dangerous builds = 0

# run without indenter

unfix           4
run		30000
Memory usage per processor = 2.065 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
   30000    0.1220056   -3.0408195            0   -2.9365338   0.80726384    486.26601 
   31000   0.11523899   -3.0452254            0   -2.9467235  -0.45196679    488.03016 
   32000   0.11671309   -3.0341159            0    -2.934354  -0.43181326    492.18636 
   33000    0.1222407   -3.0522595            0   -2.9477728 0.0026848443      483.854 
   34000   0.11512572   -3.0460203            0   -2.9476152  -0.21245818    493.13647 
   35000   0.12254508   -3.0524445            0   -2.9476977  -0.40908297    491.35424 
   36000   0.11662073   -3.0476077            0   -2.9479248  -0.00681441    487.04397 
   37000   0.12068279   -3.0633798            0   -2.9602248  -0.42268002    479.44382 
   38000   0.11671309   -3.0719801            0   -2.9722182  -0.37892984    481.83063 
   39000   0.12550174   -3.0797649            0   -2.9724908  -0.20439104    462.53227 
   40000   0.11787623   -3.0733224            0   -2.9725663  -0.34034574    467.47074 
   41000   0.11527048   -3.0710921            0   -2.9725633  -0.34310742    466.58893 
   42000   0.11312036   -3.0799073            0   -2.9832163  -0.19115407    463.84361 
   43000   0.12076996   -3.0752802            0   -2.9720506  -0.45925901    466.21436 
   44000   0.12008601   -3.0854737            0   -2.9828287  -0.42730211    465.06031 
   45000   0.11523031   -3.0813219            0   -2.9828274  -0.25270677     464.6103 
   46000   0.11474818   -3.0809077            0   -2.9828253  -0.42749761    466.13298 
   47000   0.11255445   -3.0789955            0   -2.9827882  -0.21266892    464.50422 
   48000   0.11846657   -3.0840872            0   -2.9828265  -0.26492346    464.59321 
   49000   0.11649089   -3.0718217            0   -2.9722497  -0.42141906    467.89742 
   50000   0.11857682   -3.0736036            0   -2.9722486   -0.1389822    464.85208 
   51000   0.12327382   -3.0776206            0   -2.9722508  -0.30974423    465.46077 
   52000   0.11600223   -3.0823411            0   -2.9831868  -0.45359158    465.40117 
   53000   0.11363768    -3.080283            0   -2.9831499  -0.24565163    464.66219 
   54000   0.11563656   -3.0820291            0   -2.9831873  -0.52399163    465.73246 
   55000   0.10932144     -3.07663            0   -2.9831862  -0.28497633    464.77274 
   56000   0.11442216   -3.0809919            0   -2.9831882  -0.24532139    465.43717 
   57000   0.11466454   -3.0811996            0   -2.9831888  -0.44276747    467.24929 
   58000   0.12266453   -3.0880404            0   -2.9831915  -0.24936044    464.24984 
   59000   0.10932278   -3.0766304            0   -2.9831854  -0.24813701    465.04486 
   60000   0.11984215   -3.0856269            0   -2.9831904  -0.38791762    465.21812 
Loop time of 0.850555 on 4 procs for 30000 steps with 420 atoms

Pair  time (%) = 0.43598 (51.2583)
Neigh time (%) = 0.0184039 (2.16375)
Comm  time (%) = 0.251242 (29.5386)
Outpt time (%) = 0.000487506 (0.0573163)
Other time (%) = 0.144442 (16.9821)

Nlocal:    105 ave 110 max 96 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost:    96 ave 99 max 92 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs:    892.75 ave 999 max 763 min
Histogram: 1 0 1 0 0 0 0 0 0 2

Total # of neighbors = 3571
Ave neighs/atom = 8.50238
Neighbor list builds = 631
Dangerous builds = 0
